When Jackson became President, he selected Branch as his Secretary of the Navy. In that post, Branch promoted several reforms in the Navy's policies and administration, many of which were not implemented until years later. He reduced the resources going to the construction of new ships, while increasing those applied to keeping existing vessels in good repair. Branch also sent the frigate USS Potomac to the Far East to punish the murderers of a U.S. merchant ship's crew and to generally promote and protect American commerce in the region.